Table 2. . Tissue files used in the lithium and warfarin experiments.
| Tissue | ENCODE | REMC | |
|---|---|---|---|
| Lithium | |||
| Frontal lobe | Brain_Mid_Frontal_Lobe | H1-hESC:SK-N-SH | |
| Insula | Brain_Cingulate_Gyrus | H1-hESC:SK-N-SH | |
| Temporal cortex | Brain_Inferior_Temporal_Lobe | H1-hESC:SK-N-SH | |
| Cingulate cortex | Brain_Cingulate_Gyrus | H1-hESC:SK-N-SH | |
| Amygdala including_ amygdalo-hippocampal transition area |
Brain_Inferior_Temporal_Lobe | H1-hESC:SK-N-SH | |
| Hippocampal formation including parahippocampal gyrus | Brain_Hippocampus_Middle | H1-hESC:SK-N-SH | |
| Anterior caudate and putamen | Brain_Anterior_Caudate | H1-hESC:SK-N-SH | |
| Thalamus, right | Brain_Anterior_Caudate | H1-hESC:SK-N-SH | |
| Fusiform cortex, angular gyrus | Brain_Angular_Gyrus | H1-hESC:SK-N-SH | |
| Motor cortex, substantia nigra, cerebellum | Brain_Substantia_Nigra | H1-hESC:SK-N-SH | |
| Hypothalamus | Fetal_Brain_Female Fetal_Brain_Male |
H1-hESC:SK-N-SH | |
| Warfarin | |||
| Tissue | ENCODE | REMC | GTEx |
| Liver | Adult_Liver: HepG2_Hepatocellular_Carcinoma | HepG2:liver:hepatocyte:right lobe of liver | Liver |
| Vasculature | Aorta: HUVEC_Umbilical_Vein_Endothelial_Cells | Endothelial cell of umbilical vein:dermis blood vessel endothelial cell:pulmonary artery endothelial cell:endothelial cell of coronary artery: aorta:thoracic aorta endothelial cell:vein endothelial cell:lung microvascular endothelial cell | Artery – Tibial: Artery – Coronary: Artery – Aorta |
| Small intestine | Fetal_Intestine_Small:Small_Intestine | Small intestine:Caco-2:jejunum | Small Intestine – Terminal Ileum |
The tissue file coding used in the lithium and warfarin PIP experiments, respectively. The first column contains natural language names for the tissues, while subsequent columns contain colon-delimited consortium ontology codes for related tissues and cell lines. The lithium experiment does not have tissue codes for GTEx because annotation of gene expression mapping was done manually with Allen Brain Atlas in situ hybridization data [63] in this experiment, as described herein.
PIP: Pharmacoepigenomics informatics pipeline.